Code

Changes to TRTools#1

Code

Merged

aarushi03 merged 138 commits intoaarushi03:masteraarushi03/TRTools:masterfrom gymrek-lab:mastergymrek-lab/TRTools:masterCopy head branch name to clipboardMar 8, 2023

+10,843-4,488

Commits

Commits on Feb 23, 2021

• statstr quit if no samples from the samples list in the target vcf

  gymreklab

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  0959f76

• change msg to warning for errors so they show up

  gymreklab

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  28d3e09

Commits on Feb 2, 2022

• added new field to TRRecord which holds position of full alleles

  Kulivox

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  e9e9ac4

• HipSTR harmonization sets TRRecord position to position of record without flanking bp at the start

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Commits on Feb 3, 2022

• Added correct types to mergeutils.py functions

  Kulivox

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  927f1f3

• Added multipledispatch lib to requirements

  Kulivox

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  9ad411a

• Fixed problems revealed by static type analysis and added functions that use multiple dispatch

  Kulivox

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  786bfee

• Fixed bug in compareSTR.py

  Kulivox

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  0a52fd9

• Added utility function to tr_harmonizer.py

  Kulivox

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  a8cf756

• Implemented improved record comparison, records are now harmonized before the ability to compare them is calculated, fixes HipSTR issue

  Kulivox

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  e2db6cf

• updated RELEASE_NOTES.rst

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  d098089

Commits on Feb 4, 2022

• added utility function to mergeutils.py

  Kulivox

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  9cec45a

Commits on Feb 5, 2022

• Removed multiple dispatch and created new function for choosing which harmonized record should be skipped

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  1db076d

• Added type annotations to mergeSTR.py

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  ef84886

• Added annotations that were revealed to be missing by mypy

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• mergeSTR.py now uses harmonized position to figure out which records can be merged

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  b108664

Commits on Feb 6, 2022

• added tests for additions to TRHarmonizer

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  51401ea

• removed duplicated function in mergeutils.py

  Kulivox

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  924092a

• added test for getMinHarmonizedRecords from mergeutils

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  9be775c

• updated compareSTR.py to use harmonized values UpdateComparisonResults

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  c481ac7

• added tests for comparison of harmonized HipSTR records

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  482407b

Commits on Feb 7, 2022

• removed incomplete test

  Kulivox

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  6f33b7d

• added docstring for new function in mergeutils.py

  Kulivox

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  e230a56

• Updated release notes to better describe changes

  Kulivox

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  a4cf7ce

Commits on Feb 8, 2022

• Update docs, remove extra copies of VCFs

  LiterallyUniqueLogin

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  43b5aff

• More doc cleanup

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  a77ed17

Commits on Feb 9, 2022

• added new test cases to test_mergeutils.py

  Kulivox

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  9956a7d

• Added new test cases to test_compareSTR.py

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  834e689

Commits on Feb 11, 2022

• removed HarmonizeRecords function, reordered conditions in main loop of compareSTR.py to correctly handle None Records from getNextRecords

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  6730e6a

• Merge pull request #147 from Kulivox/hipstr-flanking-bp-pos-fix

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• Bump to 4.0.2

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  2bad2b9

• Fix one bug for mergeSTR with chrX

  LiterallyUniqueLogin

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  de3f651

Commits on Feb 13, 2022

• refactored GetMinHarmonizedRecords to GetRecordComparabilityAndIncrement

  Kulivox

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  3a13eaa

• added basic overlap handler

  Kulivox

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  92be29f

Commits on Feb 15, 2022

• changed the way overlap handling works

  Kulivox

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  d1f4e5f

• Fixed crash that happened if there were no comparable records found during comparison

  Kulivox

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  eb4a8aa

• updated comments

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  0278673

• updated tests and fixed things that were revealed by them

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  f6335e5

• added comment to mergeutils tests

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  d9eb53a

• Tests for unhandled exception fix

  Kulivox

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  9823133

• Include small bug fix in 4.0.2 release

  LiterallyUniqueLogin

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  30d70fd

• Added tests for new changes to how is comparability determined

  Kulivox

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  31931aa

• added todo

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  96d8fc1

• Merge branch 'develop' into mergeSTR_harmonization_update

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  Kulivox

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  a11ef6a

• Merge pull request #149 from gymreklab/develop

  Show description for 192640c
  LiterallyUniqueLogin

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  192640c

• fixed changes broken by merge

  Kulivox

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  51885b4

Commits on Feb 17, 2022

• Added test case

  Kulivox

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  536b470

• Removed incomplete overlap handler wrapper

  Kulivox

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  865aa1b

• removed unnecessary variables

  Kulivox

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  3f21cc3

• updated types and added new function

  Kulivox

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  cc7803b

• updated mergeSTR so it correctly merges hipstr records

  Kulivox

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  e77ef75

• updated tests to reflect changes

  Kulivox

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  1424beb

Commits on Feb 24, 2022

• added end position attribute to TRRecord in tr_harmonizer.py

  Kulivox

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  f0c2e3d

• removed unused function

  Kulivox

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  922e600

• updated comparison handler in compareSTR.py

  Kulivox

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  42dcbab

• updated tests mock objects because of change in tr hramonizer

  Kulivox

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  eaf2f95

• changed type of end position from float to int in TRRecord

  Kulivox

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  4fefe7a

• updated compareSTR tests

  Kulivox

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  f5fc33a

Commits on Feb 25, 2022

• remove string case change because it was unnecessary

  Kulivox

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  9752bb1

• added case change for non harmonized values

  Kulivox

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  7427713

• changed int cast of end positions to round

  Kulivox

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  3462e4c

• fixed incorrect implementation of overlap calculation

  Kulivox

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  e4e6dd0

• added documentation of new attributes to tr_harmonizer.py

  Kulivox

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  cedd8d5

• created test confirming that merging now properly handles hipstr records with flanking bps

  Kulivox

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  bf54073

Commits on Mar 22, 2022

• added unreleased changes section and updated function docstring

  Kulivox

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  418988d

• updated RELEASE_NOTES.rst and comments in compareSTR.py

  Kulivox

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  0310ddd

Commits on Mar 24, 2022

• Merge pull request #151 from Kulivox/compareSTR-comparison-improvements

  Show description for 8dd9abf
  LiterallyUniqueLogin

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  8dd9abf

• Merge branch 'develop' into mergeSTR_harmonization_update

  LiterallyUniqueLogin

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  7aba69c

• Merge pull request #153 from Kulivox/mergeSTR_harmonization_update

  Show description for 261265f
  LiterallyUniqueLogin

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  261265f

• Update release notes

  LiterallyUniqueLogin

  committed
  ba28432

• updated mergeSTR.py to reflect changes in mergeutils.py, added explanations

  Kulivox

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  8d64c57

• updated type hints and release notes

  Kulivox

  committed
  5f7f235

• Merge pull request #155 from Kulivox/mergeSTR-mergeutils-update-fix

  Show description for 7408836
  LiterallyUniqueLogin

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  7408836

• Update CompareSTR and MergeSTR docs for HipSTR flanking changes

  LiterallyUniqueLogin

  committed
  15c57bb

• Release 4.0.3

  LiterallyUniqueLogin

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  b2259dd

Commits on Mar 25, 2022

• Actually, call it 4.1.0

  LiterallyUniqueLogin

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  1e30bf6

• Merge pull request #156 from gymreklab/develop

  Show description for ea05f91
  LiterallyUniqueLogin

  authored
  ea05f91

Commits on Jun 30, 2022

• fix the minimum position bug in mergeutils

  yli091230

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  ec17517

Commits on Aug 4, 2022

• ignore .DS_Store files

  yli091230

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  ec152a5

• Merge remote-tracking branch 'origin/develop' into statstr-samples

  LiterallyUniqueLogin

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  0dbca6f

• Add test for command line change

  LiterallyUniqueLogin

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  fe9c943

• make change to the sample vcf

  yli091230

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  1ae27f8

• new merged files

  yli091230

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  d21c611

Commits on Aug 6, 2022

• Working on adding support for Beagle. Wrote preliminary docs and added preliminary test files

  LiterallyUniqueLogin

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  4d638af

Commits on Aug 9, 2022

• Integrated Beagle into tr_harmonizer and dumpSTR. Still need harmonizer tests

  LiterallyUniqueLogin

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  8733b2f

• Add appropriate error messages and tests to tr_harmonizer

  LiterallyUniqueLogin

  committed
  a05e0ba

Commits on Aug 11, 2022

• fix the minimum position bug in mergeutils

  yli091230

  committed
  e6bfdb7

• ignore .DS_Store files

  yli091230

  committed
  2a51535

• make change to the sample vcf

  yli091230

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  1b299ec

• new merged files

  yli091230

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  b032085

• Merge branch 'yang_mergestr_bug' of github.com:yli091230/TRTools into yang_mergestr_bug

  yli091230

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  0a961d1

Commits on Aug 12, 2022

• TRTools now can successfully work with Beagle files. This features is now also tested.

  LiterallyUniqueLogin

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  109f9fa

• Refs don't work in READMEs on github, so fix

  LiterallyUniqueLogin

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  c41d5b1

Commits on Aug 17, 2022

• remove random G in gitignore

  yli091230

  committed
  307c410

Commits on Aug 18, 2022

• fix Debug function for loci is_min values are False return None value

  yli091230

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  79a4112

Commits on Aug 19, 2022

• Fix the merge debug print bug. Document changes

  LiterallyUniqueLogin

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  cb4c878

Commits on Aug 22, 2022

• Merge pull request #135 from gymreklab/statstr-samples

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  LiterallyUniqueLogin

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  dd801f5

• Merge pull request #159 from yli091230/yang_mergestr_bug

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  LiterallyUniqueLogin

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  863afa8

• Delete requirements.txt. Clarify bioconda build process in REQUIREMENTS.rst

  LiterallyUniqueLogin

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  8b65485

• Apply suggestions from code review

  Show description for fbabeee
  

  LiterallyUniqueLogin

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  aryarm

  authored
  fbabeee

• Merge pull request #166 from gymreklab/delete_requirements

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  LiterallyUniqueLogin

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  31525cc

Commits on Aug 28, 2022

• Make dependencies on tabix explicit.

  LiterallyUniqueLogin

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  413c15e

• Clarify dependency on bcftools

  LiterallyUniqueLogin

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  8c46ded

• Fix bug where dumpSTR errored out instead of gracefully failing when dealing with a mildly broken vcf

  LiterallyUniqueLogin

  committed
  f887da7

Commits on Aug 29, 2022

• Update trtools_prep_beagle_vcf.sh

  Show description for de79217
  yli091230

  authored
  de79217

• Update trtools_prep_beagle_vcf.sh

  Show description for e6caa34
  yli091230

  authored
  e6caa34

Commits on Aug 31, 2022

• Make prep for beagle script handle error conditions more cleanly and

  Show description for ab30dac
  LiterallyUniqueLogin

  committed
  ab30dac

Commits on Sep 1, 2022

• Merge branch 'develop' into beagle_for_real

  LiterallyUniqueLogin

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  76deb0d

• Merge pull request #164 from gymreklab/beagle_for_real

  Show description for dba3d94
  LiterallyUniqueLogin

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  dba3d94

• Bump to 4.2.0

  LiterallyUniqueLogin

  committed
  1f8ac36

• Merge pull request #168 from gymreklab/develop

  Show description for 1e84ea9
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  1e84ea9

• Publishing clarifications

  LiterallyUniqueLogin

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  242be0d

• Fix indentation issue in Beagle docs

  LiterallyUniqueLogin

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  4f4191c

Commits on Sep 2, 2022

• Fix cmdline test bug during bioconda build

  LiterallyUniqueLogin

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  5b5c929

• Version bump

  LiterallyUniqueLogin

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  0ef9409

Commits on Sep 5, 2022

• Add counting number of alleles to statSTR

  LiterallyUniqueLogin

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  b3548c3

• Fix flag name

  LiterallyUniqueLogin

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  385630c

• Fix error formatting

  LiterallyUniqueLogin

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  5f45948

Commits on Sep 7, 2022

• Merge pull request #170 from gymreklab/statstr_num_alleles

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  LiterallyUniqueLogin

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  757b955

Commits on Sep 22, 2022

• Address Melissa's comments

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  b8c0090

• Merge pull request #169 from gymreklab/develop

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  cf3419f

Commits on Jan 16, 2023

• Doc clarification around how to use Beagle

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  2c07013

• Doc clarification around how to use Beagle

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  16b17cd

Commits on Jan 17, 2023

• Merge pull request #173 from gymreklab/develop

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  gymreklab

  authored
  8a3cb77

Commits on Jan 24, 2023

• Start adding support for associaTR.

  LiterallyUniqueLogin

  committed
  386cae2

• First pass at getting plotting stats working again

  LiterallyUniqueLogin

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  4298fa8

Commits on Jan 25, 2023

• AssociaTR first pass! Now need to test it all, write tests and docs

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  bfb453e

Commits on Jan 26, 2023

• AssociaTR is now passing the first tests!

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  4eaba34

• Most of the associaTR tests are done and pass

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  6d9037f

Commits on Jan 27, 2023

• associaTR dosage tests pass

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  b601cb0

• Got associaTR mostly fully tested

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  d3970db

• A few small changes to associaTR, and wrote the associaTR docs

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  0d15c05

• Bump version

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  09c4e31

Commits on Jan 31, 2023

• Merge pull request #174 from gymreklab/associaTR

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• Fix a docs bug

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  bf75f5e

Commits on Feb 1, 2023

• Fix a bug in QCstr relating to outdated numpy code. Add command line tests for associaTR. Add version flag to associaTR.

  LiterallyUniqueLogin

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  9fedb40

• Bump version

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• Merge pull request #176 from gymreklab/v5.0.1

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  gymreklab

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